WARNING: if you’re running this notebook on
try.cameo.bio, things might run very slow due
to our inability to provide access to the
CPLEX
solver on a public webserver. Furthermore, Jupyter kernels might crash
and restart due to memory limitations on the server. To avoid that, we
encourage the users to shutdown previously opened notebooks. You can do
from the Home page that by selecting the notebooks highlighted in
green and pressing the Shutdown button on the top of the menu.

Users primarily interested in using cameo as a tool for enumerating
metabolic engineering strategies have access to cameo’s advanced
programming interface via cameo.api that provides access to
potential products (cameo.api.products), host organisms
(cameo.api.hosts) and a configurable design function
(cameo.api.design). Running cameo.api.design requires only
minimal input and will run the following workflow.

Currently the following host organisms and respective models are
available in cameo. More hosts and models will be added in the future
(please get in touch with us if you’d like to get a particular host
organism included).

For demonstration purposes, we’ll set a few options to limit the
computational time. Also we’ll create a multiprocessing view to take
advantage of multicore CPUs (strain design algorithms will be run in
parallel for individually predicted heterologous pathways).